But the Covid-19 Vaccine Independent Safety Monitoring Board ruled the benefits of vaccination for Covid-19 continue to greatly outweigh the risk of such rare side effects.
Medsafe said there had been about 30 cases of myocarditis per million vaccinations in New Zealand.
Helen Petousis Harris said using Nairn's death and image in this way was unacceptable.
"We do have a good handle on the kind of risk, which of course is extremely rare and also very clearly outweighed by the risks from the disease even in this younger group, in the poster it does not give any context."
Jamie Barghash owns The Bridge cafe, which was nearby the billboard. He said it was put up about a month ago.
"You see, someone had a Pfizer vaccine and passed away just like this guy in a billboard, but on the other hand millions of people didn't get the vaccine and they passed away."
The Advertising Standards Authority (ASA) has confirmed it has received four complaints about the billboard, which are now being considered by the chair of its complaints board.
If they are accepted, the authority will request a response from the advertiser and the billboard company and the matter will go before the board for determination.
In a statement, billboard company Jolly said it did not comment on specific advertising and respected and adhered to ASA rulings.
It was not the first time the ASA has had to consider complaints around Voices for Freedom ads - last year, it did not uphold complaints regarding the lobby group's billboards around free speech.
Ōrakei ward councillor Desley Simpson said because this was a medical matter, it was different.
"I'm terribly sad that someone has put that billboard up, I believe there's probably an unfortunate story behind the reason for them doing that, but I think the message unfortunately is contrary to that medical advice. I believe the right thing is for Aucklanders to follow medical advice and to get two vaccine shots and a booster."
RNZ contacted members of Nairn's family who did not wish to comment.